Here are my thoughts. I am now starting to think you don't have issue with IR level, you likely have an issue with RF interference or possibly a ground loop. Do you have anything plugged into the extender besides the emitter you are testing?
Try changing the channel/id on the extender to other values to see if that improves things. Note that you will need to setup your configuration to match the values you choose. I think that you may have to do this for every activity/device that contains IR codes. System properties may not be enough.